I haven't read all of this thread because it takes too long to infinitely load all of them but I had an issue where my infant sim had the "sit up" milestone register basically every time she did tummy time over the course of three hours, but the milestone never registered in her sim panel and she was not eligible for interactions like sitting in the high chair.
It was weird, because the blanket would disappear and she would be visibly sitting up, but the interactions available with her were all ones related to tummy time and not e.g. "practice standing" or even crawling. If an adult sim picked her up and put her back down again, it would be as if she had reverted and could no longer sit up. I moved out the entire household and moved them back in, and that seemed to fix it; she got the milestone and it registered the next time she tried tummy time.
I didn't try it without my script mods, but all I have installed is MCCC and a couple of very light introspection mods for reading out values (basically I just play basegame but use mods to try and figure out what's wrong in cases exactly like this lol).